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Yorodumi- PDB-5l96: Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l96 | |||||||||
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Title | Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-methylpyridine derivative 1 | |||||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | |||||||||
Keywords | TRANSCRIPTION / four helical bundle | |||||||||
Function / homology | Function and homology information chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Lolli, G. / Marchand, J.-R. / Caflisch, A. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: J. Med. Chem. / Year: 2016 Title: Derivatives of 3-Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation. Authors: Marchand, J.R. / Lolli, G. / Caflisch, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l96.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l96.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 5l96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/5l96 ftp://data.pdbj.org/pub/pdb/validation_reports/l9/5l96 | HTTPS FTP |
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-Related structure data
Related structure data | 5l8tC 5l8uC 5l97C 5l98C 5l99C 4ir5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13531.574 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168) Mutation: First two residues SM derive from the expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8 |
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#2: Chemical | ChemComp-6RZ / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 70.99 % / Mosaicity: 0.45 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG500MME (20%), PEG1000 (2%), PEG3350 (2%), PEG20000 (10%), MPD (2%) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 20, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→42.48 Å / Num. obs: 12723 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 36.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IR5 Resolution: 2.15→33.429 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.14 Å2 / Biso mean: 54.563 Å2 / Biso min: 32.13 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→33.429 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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